Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes

// C. Mårten Lindqvist 1 , Anders Lundmark 1 , Jessica Nordlund 1 , Eva Freyhult 2 , Diana Ekman 3 , Jonas Carlsson Almlöf 1 , Amanda Raine 1 , Elin Övernäs 1 , Jonas Abrahamsson 4, 9 , Britt-Marie Frost 5, 9 , Dan Grandér 6 , Mats Heyman 7, 9 , Josefine Palle 1, 5, 9 , Erik Forestier 8, 9 , Gudmar Lönnerholm 5, 9 , Eva C. Berglund 1, * , Ann-Christine Syvänen 1, * 1 Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden 2 Cancer Pharmacology and Computational Medicine, Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden 3 Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden 4 Department of Pediatrics, Queen Silvia Children’s Hospital, Gothenburg, Sweden 5 Department of Women’s and Children’s Health, University Children’s Hospital, Uppsala, Sweden 6 Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden 7 Childhood Cancer Research Unit, Department of Women and Child Health, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden 8 Department of Medical Biosciences, University of Umeå, Umeå, Sweden 9 Nordic Society of Pediatric Hematology and Oncology * These authors contributed equally to this work Correspondence to: Ann-Christine Syvänen, email: ann-christine.syvanen@medsci.uu.se Keywords: acute lymphoblastic leukemia, targeted next generation sequencing, somatic mutation, relapse, clonal evolution Received: June 25, 2016 Accepted: August 25, 2016 Published: August 31, 2016 ABSTRACT To characterize the mutational patterns of acute lymphoblastic leukemia (ALL) we performed deep next generation sequencing of 872 cancer genes in 172 diagnostic and 24 relapse samples from 172 pediatric ALL patients. We found an overall greater mutational burden and more driver mutations in T-cell ALL (T-ALL) patients compared to B-cell precursor ALL (BCP-ALL) patients. In addition, the majority of the mutations in T-ALL had occurred in the original leukemic clone, while most of the mutations in BCP-ALL were subclonal. BCP-ALL patients carrying any of the recurrent translocations ETV6-RUNX1 , BCR-ABL or TCF3-PBX1 harbored few mutations in driver genes compared to other BCP-ALL patients. Specifically in BCP-ALL, we identified ATRX as a novel putative driver gene and uncovered an association between somatic mutations in the Notch signaling pathway at ALL diagnosis and increased risk of relapse. Furthermore, we identified EP300 , ARID1A and SH2B3 as relapse-associated genes. The genes highlighted in our study were frequently involved in epigenetic regulation, associated with germline susceptibility to ALL, and present in minor subclones at diagnosis that became dominant at relapse. We observed a high degree of clonal heterogeneity and evolution between diagnosis and relapse in both BCP-ALL and T-ALL, which could have implications for the treatment efficiency.